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The values of bind free energr of protein-protein system are used to be positive, but change greatly after adjusting df slightly in the code. I have to say that the calculation result of this script i…
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Dear Sir
I hope this quey finds you well
I have an enzyme-ligabd compkex with a Zn atoms in the pocket. When I tried to calculate MMGBSA I got a postive values. MD simulation inputs were generated…
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I used gmx_MMPBSA for calculating the binding free energy between RNA and protein for 2500 frames using 5ns of trajectory as input. PBC was removed and the trajectory was fitted. The command used wa…
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### Bug summary
Hello, I'm new to gmx_MMPBSA. I used one of the examples for the QM calculation, and I downloaded all the sample files, but when I ran the command, I faced the following error
I us…
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![image](https://user-images.githubusercontent.com/69500371/143442056-4a30b450-5742-4fe2-b46a-21363915af57.png)
I have encountered this error whil running gmx_MMPBSA.
The command used was
gmx_…
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I was running this command,
nohup mpirun -np 8 gmx_MMPBSA MPI -O -i mmgbsa_5frames.in -cs sys.pdb -ci
prot_rna_dna.ndx -cg 1 15 -ct
fnrna-dna_0-500ns_norest-350-400_nopbc_compact_fit_dt1ns.xtc -cp…
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**Describe the issue**
I am interested to extract protein ligand each frame mmgbsa evergy value. My aim is to prepare a table of 10k frames vs mmgbsa energy in excel. requesting you kindly guide me h…
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Hello, When I perform MM_GBSA with the complex system with ligand contains the halogen atom, it will produce such error:
```
File "/home/chenzhao/miniconda/envs/mmgbsa/bin/gmx_MMPBSA", line 8, i…
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I try to use gmx_MMPBSA v1.4.3 to do MMGBSA computation and energy decomposition for a protein-ligand complex with multiple trajectories. The input files were from GROMACS 2020, and the MD simulation …
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### Documentation Link
_No response_
### Problem
Hi,
I am facing an error while running gmx_MMPBSA_ana. I have installed the latest version of gmx_MMPBSA.
The module PyQt5 is installed …